Epigenetically-regulated Arabidopsis Dicer isoforms: distinct localizations and functions in RNA silencing

Speaker: Nathan Pumplin, ETH Zurich
Host: Peter Brodersen, SCARB

RNA silencing is an ancient pathway with key roles in regulating endogenous gene expression and defending against invasive nucleic acids from transposons and viruses. In plants, silencing pathways may act through transcriptional gene silencing by modifying DNA, or post-transcriptionally by targeting expressed mRNAs. Both pathways are triggered when host Dicer-like proteins (DCLs) cleave double-stranded RNA into small interfering RNAs (siRNAs), which guide Argonaute effector proteins (AGOs) to complementary nucleotide sequences.

To understand how subcellular localization regulates silencing pathways, we created a panel of transgenic Arabidopsis lines expressing fluorescent fusions to DCL proteins. These experiments revealed that DCL4, the main anti-viral dicer, is primarily expressed from a previously-unreported transcriptional start site (TSS) isoform encoding a cytoplasmic protein.

A second DCL4 transcript isoform, encoding a nuclear-localized protein, is under epigenetic regulation via promoter methylation, and induced developmentally or by infection with a bacterial pathogen. Alternative DCL4 isoforms produce distinct siRNA populations, whose roles in development and fine-tuning of gene expression will be discussed.